Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 3Q5H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY* 3.3 0.4 - - - -
20A ILE 2.7 36.6 + - - +
23A PRO 4.5 4.2 - - - +
24A PRO* 1.3 72.8 - - - +
26A THR* 1.3 61.5 + - - +
27A PHE* 3.2 22.2 - - + -
54A LYS* 4.6 7.8 - - - +
55A LEU 3.7 5.9 + - - -
56A PHE* 3.5 22.7 - - + +
57A ASP* 2.8 50.9 - - - +
60A ASP* 4.3 13.2 - - + +
61A SER* 4.5 6.8 - - - -
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.6 35.3 + - + +
18A ILE 3.1 6.1 - - - +
19A GLY* 4.1 5.6 - - - -
24A PRO* 4.0 10.9 + - + +
25A GLN* 1.3 71.9 - - - +
27A PHE* 1.3 72.4 + - - +
54A LYS* 3.1 39.5 + - - +
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 3.4 0.7 - - - +
17A GLU* 3.1 9.9 - - - -
18A ILE* 2.8 36.4 + - + +
20A ILE* 3.8 27.1 - - + -
25A GLN* 3.2 35.7 - - + -
26A THR* 1.3 75.2 - - - +
28A LYS* 1.3 64.0 + - - +
29A VAL* 3.8 8.4 + - + -
40A VAL* 3.7 29.2 - - + -
54A LYS* 3.5 43.1 - - + -
55A LEU 3.8 6.1 - - - -
56A PHE* 3.6 31.2 - + + -
118A ASP* 3.7 9.4 - - + +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.1 42.2 + - + -
16A GLY 3.3 7.2 - - - +
17A GLU* 5.6 3.8 - - + -
27A PHE* 1.3 72.9 - - - +
29A VAL* 1.3 58.1 + - - +
54A LYS* 6.5 1.1 - - - -
116A GLU 3.8 13.9 + - - +
117A PHE* 3.9 3.4 - - - -
118A ASP* 2.6 55.4 + - - +
119A GLY 3.1 7.6 + - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.3 8.0 - - - +
16A GLY 2.9 37.7 + - - +
18A ILE* 4.1 27.6 - - + -
27A PHE* 4.2 8.5 - - + -
28A LYS* 1.3 79.7 - - - +
30A VAL* 1.3 59.7 + - - +
31A PHE* 3.8 19.3 - - + -
38A VAL* 6.2 0.2 - - + -
39A TRP 4.8 0.2 - - - +
40A VAL* 4.3 4.7 - - + -
117A PHE* 4.3 1.1 - - - -
119A GLY* 3.1 25.8 - - - +
120A VAL 4.0 2.5 - - - +
121A VAL* 3.6 28.9 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR 3.8 18.6 - - - +
15A TYR* 4.4 0.4 - - + -
29A VAL* 1.3 71.9 - - - +
31A PHE* 1.3 64.9 + - - +
32A ASP* 4.5 4.5 - - + -
117A PHE* 3.5 41.1 - - + -
119A GLY 3.2 5.4 + - - +
120A VAL* 3.4 12.0 - - + +
121A VAL 2.8 28.2 + - - +
155A TYR* 5.5 0.7 - - - +
216A THR 4.7 1.1 - - - +
217A GLY* 4.1 13.9 - - - -
335A RX6 3.8 38.8 - - + +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.4 7.2 - - + -
6A LEU* 3.9 29.4 - - + -
14A TYR 4.7 2.2 + - - -
15A TYR* 5.2 0.7 - - - -
16A GLY* 4.0 7.9 - - - -
17A GLU 4.6 0.4 - - - -
18A ILE* 3.9 13.0 - - + -
29A VAL* 3.8 28.7 - - + -
30A VAL* 1.3 73.3 - - - +
32A ASP* 1.4 51.9 + - - +
91A VAL* 4.2 22.7 - - + -
121A VAL* 3.4 34.1 - - + -
123A MET* 4.2 9.6 - - + -
153A PHE* 3.6 24.6 - - + -
155A TYR* 4.2 1.7 + - - +
165A ILE* 4.1 24.2 - - + -
167A LEU* 6.1 0.4 - - + -
216A THR* 2.7 32.4 + - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 4.4 4.3 - - + +
31A PHE* 1.4 70.8 - - - +
33A THR* 1.3 54.4 + - - +
34A GLY 3.1 1.7 + - - -
35A SER* 2.6 39.7 + - - +
75A TYR* 4.3 2.1 - - - -
120A VAL* 3.8 17.0 - - + +
121A VAL 3.0 10.0 + - - +
123A MET* 2.6 28.6 + - - +
215A ASP* 2.9 13.7 - - - +
216A THR* 3.6 1.3 - - - -
217A GLY* 3.3 9.3 - - - +
335A RX6 2.8 51.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il